AminoAcidResidue Class Reference

#include <Protein.h>

Inheritance diagram for AminoAcidResidue:

Detailed Description

amino acid residue building block for protein polypeptide chain molecules

AminoAcidResidue has three unsatisfied BondCenters: 1) "bondN" at the amino nitrogen, for the preceding amino acid residue 2) "boncC" at the carbonyl carbon, for the next amino acid residue 3) "bondCA" at the alpha carbon, for the side chain

The decision of which atoms bond to bond centers bond1, bond2, bond3 etc., depends upon several criteria: 1) chirality - in quadravalent atoms (e.g. alpha carbon), bonds 2, 3, 4 are aranged clockwise when viewed down bond 1. 2) inboard bond - unless explicitly changed, bond1 is the inboard bond for a given compound 3) dihedral angle definition - the dihedral angle for bond1 is defined relative to the plane containing bond2. bonds2,3,4... are defined relative to bond1

Public Member Functions

AminoAcidResidue (String name, String threeLetterCode="Unk", char oneLetterCode= '?')

AminoAcidResidue & setDefaultPhiAngle (Angle phi)

Set default (initial) phi dihedral angle (rotation about N-CA bond).

AminoAcidResidue & setDefaultPsiAngle (Angle psi)

Static Public Member Functions

static AminoAcidResidue create (char oneLetterCode)

Factory method for creating caninical amino acid residues.

static AminoAcidResidue create (const PdbResidue &)

Factory method for creating caninical amino acid residues.

Classes

class Alanine

class Arginine

class Asparagine

class Aspartate

class Cysteine

class Glutamate

class Glutamine

class Glycine

class Histidine

class Isoleucine

class Leucine

class Lysine

class Methionine

class Phenylalanine

class Proline

class Serine

class Threonine

class Tryptophan

class Tyrosine

class Valine

Constructor & Destructor Documentation

AminoAcidResidue	(	String	name,
		String	threeLetterCode = `"Unk"`,
		char	oneLetterCode = `'?'`
	)			`[inline]`

Parameters:

name	name of this type of amino acid. e.g. "glycine"
threeLetterCode	three letter code. Might appear in ResidueName field of PDB files
oneLetterCode	one letter code (use 'X' for non-canonical residues)

Member Function Documentation

static AminoAcidResidue create ( char oneLetterCode ) [static]

Factory method for creating caninical amino acid residues.

Parameters:

oneLetterCode

one letter code of desired amino acid residue, e.g. "W" for tryptophan

Referenced by Protein::initialize().

static AminoAcidResidue create ( const PdbResidue & ) [static]

Factory method for creating caninical amino acid residues.

AminoAcidResidue& setDefaultPhiAngle ( Angle phi ) [inline]

Set default (initial) phi dihedral angle (rotation about N-CA bond).

Phi and psi angles are offset 180 degrees from other dihedral definitions

Referenced by AminoAcidResidue::Proline::Proline().

AminoAcidResidue& setDefaultPsiAngle ( Angle psi ) [inline]

The documentation for this class was generated from the following file:

Protein.h


Public Member Functions
	AminoAcidResidue (String name, String threeLetterCode="Unk", char oneLetterCode= '?')
AminoAcidResidue &	setDefaultPhiAngle (Angle phi)
	Set default (initial) phi dihedral angle (rotation about N-CA bond).
AminoAcidResidue &	setDefaultPsiAngle (Angle psi)
Static Public Member Functions
static AminoAcidResidue	create (char oneLetterCode)
	Factory method for creating caninical amino acid residues.
static AminoAcidResidue	create (const PdbResidue &)
	Factory method for creating caninical amino acid residues.
Classes
class	Alanine
class	Arginine
class	Asparagine
class	Aspartate
class	Cysteine
class	Glutamate
class	Glutamine
class	Glycine
class	Histidine
class	Isoleucine
class	Leucine
class	Lysine
class	Methionine
class	Phenylalanine
class	Proline
class	Serine
class	Threonine
class	Tryptophan
class	Tyrosine
class	Valine